Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: M3M6Z

Calculation Name: 4BG5-A-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BG5

Chain ID: A

ChEMBL ID:

UniProt ID: O50954

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 205
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2405697.75977
FMO2-HF: Nuclear repulsion 2323213.682975
FMO2-HF: Total energy -82484.076795
FMO2-MP2: Total energy -82725.086612


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:20:ACE )


Summations of interaction energy for fragment #1(A:20:ACE )
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-7.058-4.7811.015-1.539-1.753-0.002
Interaction energy analysis for fragmet #1(A:20:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.039
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A22ASP -1-0.823-0.9143.865-0.5901.117-0.006-0.835-0.866-0.003
4A23LYS 10.9230.9712.458-6.687-6.2641.011-0.633-0.8010.001
5A24LEU 00.0750.0295.2310.1370.1370.0000.0000.0000.000
6A25PHE 00.0080.0047.2230.1780.1780.0000.0000.0000.000
7A26GLU -1-0.902-0.9508.9610.1430.1430.0000.0000.0000.000
8A27ILE 0-0.007-0.0087.5800.0470.0470.0000.0000.0000.000
9A28LEU 00.0030.01311.1990.0560.0560.0000.0000.0000.000
10A29ALA 0-0.027-0.01813.2670.0510.0510.0000.0000.0000.000
11A30ARG 10.8580.93711.4790.0600.0600.0000.0000.0000.000
12A31GLU -1-0.855-0.95815.002-0.042-0.0420.0000.0000.0000.000
13A32MET 00.0240.01516.8250.0080.0080.0000.0000.0000.000
14A33THR 0-0.085-0.02418.7470.0160.0160.0000.0000.0000.000
15A34ILE 00.004-0.00518.4880.0140.0140.0000.0000.0000.000
16A35ILE 00.0550.02420.5200.0080.0080.0000.0000.0000.000
17A36LYS 10.9370.96923.1220.0920.0920.0000.0000.0000.000
18A37LYS 10.9260.96023.4650.0400.0400.0000.0000.0000.000
19A38GLU -1-0.879-0.95124.562-0.053-0.0530.0000.0000.0000.000
20A39LYS 10.8370.92225.5990.1060.1060.0000.0000.0000.000
21A40LEU 0-0.026-0.00529.1680.0020.0020.0000.0000.0000.000
22A41GLN 0-0.0080.01631.2050.0020.0020.0000.0000.0000.000
23A42THR 0-0.0010.00333.140-0.002-0.0020.0000.0000.0000.000
24A43GLU -1-0.788-0.83136.505-0.033-0.0330.0000.0000.0000.000
25A44ILE 00.0090.01337.6310.0010.0010.0000.0000.0000.000
26A45PRO 00.0590.02040.943-0.001-0.0010.0000.0000.0000.000
27A46SER 0-0.040-0.04443.385-0.001-0.0010.0000.0000.0000.000
28A47GLN 00.0600.01439.6260.0010.0010.0000.0000.0000.000
29A48PHE 00.010-0.00436.5860.0000.0000.0000.0000.0000.000
30A49GLY 00.0260.02240.0980.0020.0020.0000.0000.0000.000
31A50LEU 00.0350.02136.7140.0010.0010.0000.0000.0000.000
32A51LYS 10.9400.98941.1800.0220.0220.0000.0000.0000.000
33A52ASN 0-0.031-0.02643.183-0.001-0.0010.0000.0000.0000.000
34A53SER 0-0.026-0.05242.4790.0010.0010.0000.0000.0000.000
35A54MET 00.0130.01935.782-0.002-0.0020.0000.0000.0000.000
36A55PHE 0-0.025-0.03535.692-0.002-0.0020.0000.0000.0000.000
37A56GLU -1-0.928-0.95940.648-0.024-0.0240.0000.0000.0000.000
38A57LEU 0-0.0250.00140.7610.0000.0000.0000.0000.0000.000
39A58LEU 0-0.045-0.02736.468-0.001-0.0010.0000.0000.0000.000
40A59ASN 0-0.014-0.02140.2310.0000.0000.0000.0000.0000.000
41A60VAL 0-0.0040.02336.137-0.002-0.0020.0000.0000.0000.000
42A61TYR 00.0170.00037.8000.0020.0020.0000.0000.0000.000
43A62LYS 10.9410.95835.3980.0680.0680.0000.0000.0000.000
44A63NME 00.0230.03738.0830.0000.0000.0000.0000.0000.000
45A70ACE 00.021-0.00146.0230.0010.0010.0000.0000.0000.000
46A71LEU 0-0.028-0.02241.844-0.002-0.0020.0000.0000.0000.000
47A72GLN 00.011-0.01642.0390.0000.0000.0000.0000.0000.000
48A73GLU -1-0.934-0.93742.349-0.036-0.0360.0000.0000.0000.000
49A74LYS 10.9340.97342.4440.0280.0280.0000.0000.0000.000
50A75MET 0-0.050-0.01135.455-0.002-0.0020.0000.0000.0000.000
51A76ASN 00.023-0.00739.474-0.002-0.0020.0000.0000.0000.000
52A77SER 0-0.0190.00742.0430.0000.0000.0000.0000.0000.000
53A78SER 00.041-0.00741.701-0.001-0.0010.0000.0000.0000.000
54A79LEU 00.0290.04239.647-0.002-0.0020.0000.0000.0000.000
55A80ALA 00.0540.01136.985-0.001-0.0010.0000.0000.0000.000
56A81GLU -1-0.874-0.95034.996-0.062-0.0620.0000.0000.0000.000
57A82SER 0-0.047-0.01834.668-0.001-0.0010.0000.0000.0000.000
58A83GLN 00.0060.00835.5150.0010.0010.0000.0000.0000.000
59A84LYS 10.8960.94929.2420.0830.0830.0000.0000.0000.000
60A85MET 00.008-0.00531.4120.0000.0000.0000.0000.0000.000
61A86ARG 10.8210.90532.7410.0400.0400.0000.0000.0000.000
62A87ARG 10.8210.89526.1160.0790.0790.0000.0000.0000.000
63A88GLN 0-0.0160.00427.0260.0070.0070.0000.0000.0000.000
64A89PHE 00.0630.03028.0370.0000.0000.0000.0000.0000.000
65A90TYR 0-0.013-0.02029.9760.0040.0040.0000.0000.0000.000
66A91SER 0-0.033-0.03825.7360.0020.0020.0000.0000.0000.000
67A92SER 0-0.025-0.01125.4030.0010.0010.0000.0000.0000.000
68A93LEU 0-0.007-0.01625.6630.0040.0040.0000.0000.0000.000
69A94SER 0-0.026-0.01724.3670.0030.0030.0000.0000.0000.000
70A95TYR 0-0.071-0.04926.3950.0040.0040.0000.0000.0000.000
71A96ASN 0-0.007-0.00729.5330.0020.0020.0000.0000.0000.000
72A97THR 00.019-0.01131.1540.0000.0000.0000.0000.0000.000
73A98THR 0-0.047-0.01834.715-0.001-0.0010.0000.0000.0000.000
74A99ASP -1-0.720-0.82830.839-0.001-0.0010.0000.0000.0000.000
75A100ILE 0-0.042-0.01231.775-0.001-0.0010.0000.0000.0000.000
76A101PHE 0-0.024-0.02035.208-0.001-0.0010.0000.0000.0000.000
77A102ASN 0-0.021-0.02936.8030.0010.0010.0000.0000.0000.000
78A103LEU 00.0640.03533.5420.0010.0010.0000.0000.0000.000
79A104ALA 0-0.036-0.00537.366-0.001-0.0010.0000.0000.0000.000
80A105GLU -1-0.952-0.96740.051-0.001-0.0010.0000.0000.0000.000
81A106ILE 00.0290.01938.2820.0000.0000.0000.0000.0000.000
82A107VAL 00.021-0.00838.2110.0000.0000.0000.0000.0000.000
83A108ASN 00.0480.06041.189-0.002-0.0020.0000.0000.0000.000
84A109LYS 10.8320.92744.4130.0030.0030.0000.0000.0000.000
85A110LEU 00.0500.00640.5780.0000.0000.0000.0000.0000.000
86A111TYR 0-0.025-0.01044.574-0.001-0.0010.0000.0000.0000.000
87A112LYS 10.9020.96445.9330.0060.0060.0000.0000.0000.000
88A113ASP -1-0.855-0.92847.773-0.008-0.0080.0000.0000.0000.000
89A114PRO 00.019-0.01247.120-0.001-0.0010.0000.0000.0000.000
90A115LYS 10.8980.96646.5910.0080.0080.0000.0000.0000.000
91A116ALA 00.0580.04743.7680.0000.0000.0000.0000.0000.000
92A117HIS 0-0.029-0.02442.928-0.002-0.0020.0000.0000.0000.000
93A118ASP -1-0.898-0.96439.506-0.023-0.0230.0000.0000.0000.000
94A119THR 0-0.015-0.05738.272-0.002-0.0020.0000.0000.0000.000
95A120ILE 00.0050.01437.410-0.001-0.0010.0000.0000.0000.000
96A121LYS 10.9340.97137.1790.0250.0250.0000.0000.0000.000
97A122LYS 10.8670.95533.7610.0210.0210.0000.0000.0000.000
98A123ILE 00.0630.03132.598-0.002-0.0020.0000.0000.0000.000
99A124SER 0-0.039-0.02132.696-0.002-0.0020.0000.0000.0000.000
100A125GLY 00.024-0.00330.259-0.005-0.0050.0000.0000.0000.000
101A126GLY 00.0760.03727.555-0.005-0.0050.0000.0000.0000.000
102A127ILE 0-0.043-0.01727.072-0.006-0.0060.0000.0000.0000.000
103A128ARG 10.9060.95627.2900.0500.0500.0000.0000.0000.000
104A129ILE 00.0650.03122.607-0.009-0.0090.0000.0000.0000.000
105A130GLN 00.0130.01223.011-0.005-0.0050.0000.0000.0000.000
106A131GLN 0-0.056-0.03422.919-0.012-0.0120.0000.0000.0000.000
107A132GLY 00.0830.03022.261-0.013-0.0130.0000.0000.0000.000
108A133PHE 00.0330.01316.241-0.024-0.0240.0000.0000.0000.000
109A134GLU -1-0.863-0.94818.772-0.123-0.1230.0000.0000.0000.000
110A135VAL 00.0210.02020.542-0.014-0.0140.0000.0000.0000.000
111A136ALA 00.0240.01816.132-0.022-0.0220.0000.0000.0000.000
112A137LEU 0-0.044-0.03315.322-0.050-0.0500.0000.0000.0000.000
113A138GLU -1-1.007-0.98416.776-0.194-0.1940.0000.0000.0000.000
114A139ASP -1-0.856-0.95017.739-0.263-0.2630.0000.0000.0000.000
115A140LEU 0-0.067-0.02010.575-0.057-0.0570.0000.0000.0000.000
116A141ALA 0-0.023-0.02914.126-0.067-0.0670.0000.0000.0000.000
117A142ILE 0-0.0200.00215.802-0.007-0.0070.0000.0000.0000.000
118A143ASN 0-0.028-0.01914.9880.0130.0130.0000.0000.0000.000
119A144MET 0-0.049-0.0089.663-0.149-0.1490.0000.0000.0000.000
120A145ASP -1-0.871-0.95111.921-0.533-0.5330.0000.0000.0000.000
121A146LYS 10.9580.97514.0910.3000.3000.0000.0000.0000.000
122A147LEU 0-0.033-0.0158.820-0.004-0.0040.0000.0000.0000.000
123A148LYS 10.8960.9448.8490.3670.3670.0000.0000.0000.000
124A149ALA 0-0.0150.01210.4560.0220.0220.0000.0000.0000.000
125A150ASN 0-0.029-0.01910.366-0.114-0.1140.0000.0000.0000.000
126A151ASP -1-0.952-0.97311.449-0.263-0.2630.0000.0000.0000.000
127A152PHE 00.0040.0149.0870.0620.0620.0000.0000.0000.000
128A153ASN 0-0.014-0.01810.070-0.072-0.0720.0000.0000.0000.000
129A154LYS 11.0581.0126.8490.1960.1960.0000.0000.0000.000
130A155ASN 0-0.048-0.0196.940-0.092-0.0920.0000.0000.0000.000
131A156THR 00.0210.0199.1550.0800.0800.0000.0000.0000.000
132A157LEU 00.0080.0083.680-0.1310.0160.010-0.071-0.0860.000
133A158GLU -1-0.975-0.9825.562-0.024-0.0240.0000.0000.0000.000
134A159GLU -1-0.899-0.9546.656-0.136-0.1360.0000.0000.0000.000
135A160ILE 00.0400.0109.1360.0550.0550.0000.0000.0000.000
136A161TYR 0-0.041-0.0195.5220.1730.1730.0000.0000.0000.000
137A162ASN 00.016-0.0067.8410.2390.2390.0000.0000.0000.000
138A163LEU 00.0230.0309.9930.0650.0650.0000.0000.0000.000
139A164ILE 0-0.004-0.0039.9150.0530.0530.0000.0000.0000.000
140A165VAL 00.0170.0118.9340.0640.0640.0000.0000.0000.000
141A166ASP -1-0.827-0.86911.6630.0110.0110.0000.0000.0000.000
142A167LEU 0-0.035-0.00814.7990.0220.0220.0000.0000.0000.000
143A168THR 0-0.138-0.12612.8080.0350.0350.0000.0000.0000.000
144A169LEU 0-0.038-0.03014.3670.0260.0260.0000.0000.0000.000
145A170ILE 00.0150.01116.9920.0110.0110.0000.0000.0000.000
146A171LYS 10.8720.95619.3180.0630.0630.0000.0000.0000.000
147A172LYS 10.9340.96316.858-0.015-0.0150.0000.0000.0000.000
148A173GLU -1-0.889-0.94321.0620.0260.0260.0000.0000.0000.000
149A174TRP 0-0.0120.00723.0320.0020.0020.0000.0000.0000.000
150A175LEU 0-0.0070.01424.2350.0010.0010.0000.0000.0000.000
151A176SER 00.0180.01824.8460.0020.0020.0000.0000.0000.000
152A177THR 0-0.0180.00526.5470.0020.0020.0000.0000.0000.000
153A178ILE 0-0.034-0.02028.9240.0000.0000.0000.0000.0000.000
154A179GLU -1-0.891-0.93928.4570.0130.0130.0000.0000.0000.000
155A180THR 0-0.064-0.06429.8330.0030.0030.0000.0000.0000.000
156A181LEU 0-0.024-0.01132.4500.0000.0000.0000.0000.0000.000
157A182ILE 0-0.016-0.02133.7330.0010.0010.0000.0000.0000.000
158A183LYS 10.9480.99835.450-0.018-0.0180.0000.0000.0000.000
159A184SER 0-0.123-0.11836.9450.0000.0000.0000.0000.0000.000
160A185SER 00.014-0.00638.451-0.001-0.0010.0000.0000.0000.000
161A186ASN 0-0.033-0.01940.619-0.001-0.0010.0000.0000.0000.000
162A187ALA 0-0.0250.00241.2630.0010.0010.0000.0000.0000.000
163A188THR 00.019-0.00143.1110.0010.0010.0000.0000.0000.000
164A189LEU 00.0380.00546.800-0.001-0.0010.0000.0000.0000.000
165A190GLU -1-0.812-0.92449.4380.0020.0020.0000.0000.0000.000
166A191LEU 0-0.0110.00442.632-0.001-0.0010.0000.0000.0000.000
167A192GLN 0-0.0210.00845.2590.0000.0000.0000.0000.0000.000
168A193TYR 0-0.076-0.03646.847-0.002-0.0020.0000.0000.0000.000
169A194ASN 0-0.027-0.01349.896-0.002-0.0020.0000.0000.0000.000
170A195THR 0-0.013-0.01146.3480.0010.0010.0000.0000.0000.000
171A196GLU -1-0.932-0.94946.684-0.001-0.0010.0000.0000.0000.000
172A197LYS 10.9760.98346.597-0.003-0.0030.0000.0000.0000.000
173A198LEU 0-0.017-0.00241.7050.0010.0010.0000.0000.0000.000
174A199ASN 00.0590.03842.276-0.001-0.0010.0000.0000.0000.000
175A200ASP -1-0.865-0.91441.723-0.001-0.0010.0000.0000.0000.000
176A201HIS 00.0230.06139.2190.0010.0010.0000.0000.0000.000
177A202ILE 00.0240.06936.6810.0010.0010.0000.0000.0000.000
178A203GLU -1-0.930-0.98337.176-0.008-0.0080.0000.0000.0000.000
179A204GLN 0-0.029-0.02337.691-0.001-0.0010.0000.0000.0000.000
180A205THR 0-0.102-0.09735.3570.0020.0020.0000.0000.0000.000
181A206TYR 00.002-0.02032.1050.0020.0020.0000.0000.0000.000
182A207LYS 10.8830.95632.4970.0100.0100.0000.0000.0000.000
183A208ASP -1-0.831-0.91632.428-0.008-0.0080.0000.0000.0000.000
184A209THR 00.010-0.00727.937-0.004-0.0040.0000.0000.0000.000
185A210MET 0-0.029-0.00428.136-0.004-0.0040.0000.0000.0000.000
186A211ILE 0-0.012-0.00729.375-0.007-0.0070.0000.0000.0000.000
187A212SER 0-0.021-0.00626.852-0.005-0.0050.0000.0000.0000.000
188A213LEU 00.0100.00823.172-0.008-0.0080.0000.0000.0000.000
189A214CYS 0-0.038-0.02324.417-0.011-0.0110.0000.0000.0000.000
190A215LEU 00.0270.01125.915-0.008-0.0080.0000.0000.0000.000
191A216LYS 10.9830.99919.5390.0000.0000.0000.0000.0000.000
192A217SER 00.0350.02621.002-0.015-0.0150.0000.0000.0000.000
193A218GLU -1-1.059-1.01821.718-0.084-0.0840.0000.0000.0000.000
194A219GLN 00.063-0.01321.610-0.011-0.0110.0000.0000.0000.000
195A220THR 0-0.0220.00916.431-0.006-0.0060.0000.0000.0000.000
196A221LEU 0-0.0040.02518.197-0.028-0.0280.0000.0000.0000.000
197A222LEU 00.0040.01319.595-0.019-0.0190.0000.0000.0000.000
198A223HIS 00.0050.00816.462-0.025-0.0250.0000.0000.0000.000
199A224LEU 00.0360.00013.533-0.026-0.0260.0000.0000.0000.000
200A225ASP -1-0.894-0.93616.726-0.227-0.2270.0000.0000.0000.000
201A226THR 0-0.056-0.03418.802-0.003-0.0030.0000.0000.0000.000
202A227LEU 0-0.001-0.00712.790-0.016-0.0160.0000.0000.0000.000
203A228PHE 0-0.066-0.02112.916-0.053-0.0530.0000.0000.0000.000
204A229LYS 10.7620.87716.8090.2060.2060.0000.0000.0000.000
205A230NME 0-0.0020.00819.121-0.007-0.0070.0000.0000.0000.000